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GeneBe

S100P

S100 calcium binding protein P, the group of EF-hand domain containing|S100 calcium binding proteins

Basic information

Region (hg38): 4:6693877-6697170

Links

ENSG00000163993NCBI:6286OMIM:600614HGNC:10504Uniprot:P25815AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100P gene.

  • Inborn genetic diseases (7 variants)
  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100P gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
1
clinvar
1
missense
7
clinvar
7
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
?
0
non coding
?
0
Total 0 0 7 0 1

Variants in S100P

This is a list of pathogenic ClinVar variants found in the S100P region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
4-6693951-G-A Inborn genetic diseases Uncertain significance (May 24, 2023)2551702
4-6693994-G-A Inborn genetic diseases Uncertain significance (Mar 17, 2023)2526298
4-6694007-G-A Benign (May 24, 2018)767948
4-6694020-A-G Inborn genetic diseases Uncertain significance (May 26, 2022)2291538
4-6694043-G-C Inborn genetic diseases Uncertain significance (Jan 17, 2023)2476064
4-6696929-A-G Inborn genetic diseases Uncertain significance (May 11, 2022)2288697
4-6696945-A-G Inborn genetic diseases Uncertain significance (May 23, 2023)2550460
4-6697022-G-C Inborn genetic diseases Uncertain significance (Aug 14, 2023)2618302

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
S100Pprotein_codingprotein_codingENST00000296370 24102
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.03330.6301257230221257450.0000875
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.3786355.11.140.00000302624
Missense in Polyphen1913.6871.3881170
Synonymous0.2822223.70.9260.00000153179
Loss of Function0.29522.500.7991.93e-720

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00003610.0000352
Middle Eastern0.000.00
South Asian0.0005880.000588
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May function as calcium sensor and contribute to cellular calcium signaling. In a calcium-dependent manner, functions by interacting with other proteins, such as EZR and PPP5C, and indirectly plays a role in physiological processes like the formation of microvilli in epithelial cells. May stimulate cell proliferation in an autocrine manner via activation of the receptor for activated glycation end products (RAGE). {ECO:0000269|PubMed:14617629, ECO:0000269|PubMed:19111582, ECO:0000269|PubMed:22399290}.;
Pathway
Gastric Cancer Network 1;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

pRec
0.113

Intolerance Scores

loftool
rvis_EVS
-0.16
rvis_percentile_EVS
41.25

Haploinsufficiency Scores

pHI
0.222
hipred
N
hipred_score
0.273
ghis
0.560

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.947

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
response to organic substance;neutrophil degranulation;endothelial cell migration
Cellular component
extracellular region;nucleus;cytoplasm;nuclear body;microvillus membrane;secretory granule lumen;extracellular exosome
Molecular function
magnesium ion binding;calcium ion binding;protein binding;protein homodimerization activity;cadherin binding;transition metal ion binding;calcium-dependent protein binding;RAGE receptor binding